I'm very happy to announce that the next version of the RDKit -- 2012.09 (a.k.a Q3 2012) -- is released.
The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2012/ The files can also be downloaded from the google project page: http://code.google.com/p/rdkit/downloads/list The binaries for Windows, Python 2.6 and Python 2.7, have also been uploaded. The online version of the documentation at rdkit.org has been updated. Thanks to the everyone who submitted bug reports and suggestions for this release! Please let me know if you find any problems with the release or have suggestions for the next one. -greg ****** Release_2012.09.1 ******* (Changes relative to Release_2012.06.1) !!!!!! IMPORTANT !!!!!! - Some of the bug fixes affect the generation of SMILES. Canonical SMILES generated with this version of the RDKit will be different from previous versions. - The fix to Issue 252 (see below) will lead to changes in calculated logP and MR values for some compounds. - The fix to Issue 254 (see below) will lead to changes in some descriptors and geometries for sulfur-containing compounds. - The fix to Issue 256 (see below) has changed the name of the optional argument to mol.GetNumAtoms from onlyHeavy to onlyExplicit. For compatibility reasons, Python code that uses explicitly uses onlyHeavy will still work, but it will generate warnings. This compatibility will be removed in a future release. Acknowledgements: Gianpaolo Bravi, David Cosgrove, Andrew Dalke, Fabian Dey, James Davidson, JP Ebejer, Gabriele Menna, Stephan Reiling, Roger Sayle, James Swetnam Bug Fixes: - The molecules that come from mergeQueryHs() now reset the RingInfo structure. (issue 245) - The output from MurckoScaffold.MakeScaffoldGeneric no longer includes stereochemistry or explicit Hs. (issue 246) - D and T atoms in CTABs now have their isotope information set. (issue 247) - Some problems with ring finding in large, complex molecules have been fixed. (issue 249) - The "rootedAtAtom" argument for FindAllSubgraphsOfLengthN is now handled properly. (issue 250) - Bonds now have a SetProp() method available in Python. (issue 251) - A number of problems with the Crippen atom parameters have been fixed. (issue 252) - Ring closure digits are no longer repeated on the same atom in SMILES generated by the RDKit. (issue 253) - Non-ring sulfur atoms adjacent to aromatic atoms are no longer set to be SP2 hybridized. This allows them to be stereogenic. (issue 254) - The combineMols() function now clears computed properties on the result molecule. - A couple of problems with the pickling functions on big endian hardware were fixed. - The molecule drawing code now uses isotope information - Superscript/Subscript handling in the agg canvas has been improved. - SKP lines in CTABS are now propertly handled. (Issue 255) - The name of the optional argument to mol.GetNumAtoms has been changed from onlyHeavy to onlyExplicit. The method counts the number of atoms in the molecular graph, not the number of heavy atoms. These numbers happen to usually be the same (which is why this has taken so long to show up), but there are exceptions if Hs or dummy atoms are in the graph. (Issue 256) - Unknown bonds in SMILES are now output using '~' instead of '?'. The SMILES parser now recognizes '~' as an "any bond" query. (Issue 257) - Lines containing only white space in SDF property blocks are no longer treated as field separators. - Transition metals and lanthanides no longer have default valences assigned. New Features: - The RDKit now has a maximum common substructure (MCS) implementation contributed by Andrew Dalke. This is currently implemented in Python and is available as: from rdkit.Chem import MCS Documentation is available as a docstring for the function MCS.FindMCS and in the GettingStarted document. - A few new functions have been added to rdkit.Chem.Draw: MolsToImage(), MolsToGridImage(), ReactionToImage() - CalcMolFormula() now provides the option to include isotope information. - The RDKit and Layered fingerprinters both now accept "fromAtoms" arguments that can be used to limit which atoms contribute to the fingerprint. - Version information is now available in the Java wrapper. - The descriptor NumRadicalElectrons is now available. - The PyMol interface now supports a GetPNG() method which returns the current contents of the viewer window as an PIL Image object. - Molecules (ROMol in C++, rdkit.Chem.Mol in Python) now have a getNumHeavyAtoms() method. - Component-level grouping (parens) can be used in reaction SMARTS. New Database Cartridge Features: - support for molecule <-> pickle conversion via the functions mol_to_pkl, mol_from_pkl, and is_valid_mol_pkl. - support for bit vector <-> binary text conversion via the functions bfp_to_binary_text, bfp_from_binary_text New Java Wrapper Features: Deprecated modules (to be removed in next release): Removed modules: Other: - During this release cycle, the sourceforge project was updated to their new hosting system. This explains the change in bug/issue ids. - the SMILES parser is now substantially faster. - The molecular drawings generated by Code/Demo/RDKit/Draw/MolDrawing.h have been improved. - There is now demo code availble for using the C++ drawing code within Qt applications. (contributed by David Cosgrove) - The directory $RDBASE/Regress now contains sample data and scripts for benchmarking the database cartridge. - Fused-ring aromaticity is now only considered in rings of up to size 24. - It is no longer necessary to have flex and bison installed in order to build the RDKit. ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct _______________________________________________ Rdkit-devel mailing list Rdkitemail@example.com https://lists.sourceforge.net/lists/listinfo/rdkit-devel